Variant report

Variant	rs12279670
Chromosome Location	chr11:26931851-26931852
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10835084	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11029745	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12275216	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12275357	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12280480	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282988	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12287918	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12288441	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574167	0.92[ASN][1000 genomes]
rs12574501	0.92[ASN][1000 genomes]
rs12577148	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450220	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450221	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16916312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1822893	0.86[ASN][1000 genomes]
rs1822894	0.86[ASN][1000 genomes]
rs1901076	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2350934	0.83[JPT][hapmap]
rs4329641	0.81[ASN][1000 genomes]
rs4922777	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923405	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923408	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56361643	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58646119	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58789402	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59761353	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60690634	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888261	0.94[ASN][1000 genomes]
rs6484255	0.90[ASN][1000 genomes]
rs7101730	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108314	0.83[JPT][hapmap]
rs7111033	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9666797	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044544	chr11:26506962-26967285	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv916187	chr11:26576875-27328603	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv897146	chr11:26913936-27019331	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv983219	chr11:26926565-26932064	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
5	nsv983176	chr11:26931453-26935388	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12279670	SLC5A12	cis	cerebellum	SCAN
rs12279670	ANO3	cis	cerebellum	SCAN
rs12279670	FSHB	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:26926000-26936400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:26927200-26932200	Weak transcription	Fetal Lung	lung
3	chr11:26927200-26936200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:26928000-26932000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:26930200-26933200	Enhancers	Colon Smooth Muscle	Colon
6	chr11:26931000-26933200	Enhancers	Liver	Liver
7	chr11:26931200-26933200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:26931600-26932800	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr11:26931800-26932000	Enhancers	Stomach Smooth Muscle	stomach
10	chr11:26931800-26932800	Enhancers	Rectal Smooth Muscle	rectum
11	chr11:26931800-26933000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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